aact_studies.tsvaact_drugs.tsvaact_descriptions.tsvaact_drugs_leadmine.tsvaact_drugs_smi_pubchem_cid.tsvaact_drugs_smi_pubchem_cid2inchi.tsvaact_drugs_inchi2chembl.tsvaact_drugs_chembl_activity_pchembl.tsvaact_drugs_chembl_target_component.tsvpharos_targets.tsvaact_descriptions_tagger_matches.tsvdiseases_entities.tsv
nct_idis the study ID.
## [1] "Thu Apr 4 16:02:14 2019"
library(readr)
library(data.table)
library(plotly, quietly=T)
Read file of all studies in AACT.
## [1] "Total studies: 300214 ; unique NCT_IDs: 300214"
Reference type results_reference may offer greater evidence, confidence.
## [1] "references: 388031; NCT_IDs: 61208; PMIDs: 287758; results_references: 64880"
Read file of all drugs in AACT.
id is AACT ID.## [1] "Unique drug names: 91347 ; unique intervention IDs: 255077"
Select only Interventional studies (study_type) associated with drugs (via nct_id).
## [1] "Interventional studies: 237892 (79.2%)"
## [1] "Interventional drug studies: 124421 ; unique NCT_IDs: 124421"
| phase | N_studies | N_drugs |
|---|---|---|
| Early Phase 1 | 1574 | 2615 |
| Phase 1 | 23603 | 48593 |
| Phase 1/Phase 2 | 6663 | 13288 |
| Phase 2 | 33910 | 68850 |
| Phase 2/Phase 3 | 3305 | 6503 |
| Phase 3 | 22988 | 49507 |
| Phase 4 | 19593 | 36331 |
| NA | 12785 | 29390 |
| overall_status | N |
|---|---|
| Completed | 145006 |
| Recruiting | 33973 |
| Terminated | 19618 |
| Unknown status | 18463 |
| Active, not recruiting | 13962 |
| Not yet recruiting | 8001 |
| NA | 7080 |
| Withdrawn | 6969 |
| Enrolling by invitation | 1060 |
| Suspended | 945 |
(To do: stack with study start_year.)
## Warning: Ignoring 1 observations
## Warning: Ignoring 1 observations
AACT drug names resolved to standard names and structures via SMILES. Note that one name may include multiple chemicals. Now we can use cheminformatically rigorous counts for drugs as active pharmaceutical ingredients (APIs).
## [1] "Drug unique SMILES resolved by LeadMine: 4699 ; unique intervention IDs: 171741"
| smi2img | N_mentions | names |
|---|---|---|
| 2637 | Abraxane; PACLITAXEL; Paclitaxel; Taxol; abraxane; paclitaxel; taxol | |
| 2545 | CYCLOPHOSPHAMIDE; Ciclophosphamide; Cyclophosphamid; Cyclophosphamide; ciclophosphamide; cyclophosphamide | |
| 2461 | CISPLATIN; Cis-platinum; Cisplatin; Cisplatine; Cisplatinum; cis Platinum; cis-platinum; cisplatin; cisplatine; cisplatinum | |
| 2070 | DEXAMETHASONE; Dexamethason; Dexamethasone; Dexamethosone; Maxitrol; OZURDEX; Oradexon; Ozurdex; dexamethason; dexamethasone; dexamethosone | |
| 2054 | CARBOPLATIN; Carboplatin; Carboplatine; Paraplatin; carboplatin; carboplatine | |
| 1779 | DOCETAXEL; Docetaxel; docetaxel | |
| 1625 | METFORMIN; MetFORMIN; Metformin; Metformine; metformin; metformine | |
| 1540 | GEMCITABINE; Gemcitabine; gemcitabine | |
| 1342 | CAPECITABINE; Capecitabin; Capecitabine; XELODA; Xeloda; capecitabine; xeloda | |
| 1178 | Cortancyl; Lodotra; Meticorten; Prednison; Prednisone; RAYOS; prednison; prednisone | |
| 1157 | 0xaliplatin; Eloxatin; OXALIPLATIN; OXAliplatin; Oxaliplatin; Oxaliplatine; eloxatin; oxaliplatin; oxaliplatine | |
| 1157 | METHOTREXATE; Methotrexate; Metoject; methotrexate | |
| 1086 | BUPIVACAINE; Bupivacain; Bupivacaine; EXPAREL; Exparel; SKY0402; bupivacain; bupivacaine | |
| 1044 | ETOPOSIDE; Etoposid; Etoposide; etoposide | |
| 1027 | ADOPORT; ADVAGRAF; Adoport; Advagraf; ENVARSUS; Envarsus; FK-506; FK506; PROGRAF; Prograf; Protopic; TACROLIMUS; Tacrolimus; tacrolimus | |
| 978 | NORMAL SALINE; Normal Saline; Normal saline; normal salin; normal saline | |
| 977 | LIDOCAINE; LMX 4; LMX4; Lidocain; Lidocaine; Lidoderm; Lignocain; Lignocaine; Oraqix; lidocain; lidocaine; lignocaine | |
| 908 | CYTARABINE; Cytarabine; Cytosar; DepoCyt; DepoCyte; Depocyt; Depocyte; cytarabine; cytosar | |
| 903 | COPEGUS; Copegus; REBETOL; RIBAVIRIN; Rebetol; Ribasphere; Ribavarin; Ribavirin; Ribavirine; Virazole; rebetol; ribavarin; ribavirin | |
| 846 | Diprivan; PROPOFOL; Propofol; propofol |
## [1] "Drugs (drug names) with resolved structure: 180555 / 197300 (91.5%)"
## [1] "Mentions by intervention ID: 157862 / 171741 (91.9%)"
## [1] "Mentions by study: 92966 / 99647 (93.3%)"
## [1] "Mentions by drug name: 11108 / 58297 (19.1%)"
## [1] "PubChem SMILES2CID hits: 3960 / 4698 (84.3%)"
## [1] "Intervention IDs mapped to PubChem CIDs (via SMILES): 153876"
## [1] "PubChem CIDs with InChIKeys: 3801"
## [1] "ChEMBL compounds mapped via InChIKeys: 3332"
Select only activities with pChembl values for confidence.
## [1] "ChEMBL activities: 124438"
## [1] "ChEMBL activities molecules: 2287 ; targets: 3832 ; documents: 16198"
## [1] "ChEMBL target proteins: 3157"
## [1] "ChEMBL target proteins mapped to TCRD (human): 1806"
## [1] "Organisms: 187"
| organism | N_targets |
|---|---|
| Homo sapiens | 1806 |
| Rattus norvegicus | 529 |
| Mus musculus | 238 |
| Bos taurus | 98 |
| Sus scrofa | 36 |
| Cavia porcellus | 26 |
| Escherichia coli K-12 | 19 |
| Oryctolagus cuniculus | 18 |
| Escherichia coli | 17 |
| Mycobacterium tuberculosis | 17 |
## [1] "Human targets: 1806"
| target_type | N |
|---|---|
| SINGLE PROTEIN | 1216 |
| PROTEIN COMPLEX | 247 |
| PROTEIN FAMILY | 210 |
| PROTEIN COMPLEX GROUP | 91 |
| PROTEIN-PROTEIN INTERACTION | 16 |
| SELECTIVITY GROUP | 14 |
| CHIMERIC PROTEIN | 12 |
## [1] "Human single-protein targets: 1216 ; unique UniProts: 1216"
## [1] " Tchem: 733" " Tclin: 341" " Tbio: 140"
## [4] " Tdark: 2"
With JensenLab DOID entities dictionary. On descriptions from detailed_descriptions table.
serialno corresponds with DOID.id is AACT primary key.| doid | N_mentions | terms |
|---|---|---|
| DOID:4 | 76402 | DISEASE; Disease; dis- ease; dis-ease; disease |
| DOID:0111161 | 73734 | CAN; CaN; Can; can |
| DOID:162 | 28596 | CANCER; CANcer; Cancer; Malignant Tumor; Malignant neoplasm; Malignant tumor; Primary Cancer; Primary cancer; cancer; malignant Tumor; malignant neoplasm; malignant tumor; primary cancer |
| DOID:9351 | 17274 | DIABETES; DIABETES MELLITUS; DIAbetes; DIabetes; Diabetes; Diabetes Mellitus; Diabetes mellitus; diabetes; diabetes Mellitus; diabetes mellitus; diabetes-mellitus |
| DOID:6713 | 16632 | CVA; Cerebrovascular Accident; Cerebrovascular Disease; Cerebrovascular accident; Cerebrovascular disease; STROKE; STRokE; Stroke; cerebro- vascular disease; cerebro-vascular disease; cerebrovascular accident; cerebrovascular disease; cerebrovascular disorder; cerebrovascular syndrome; cv-a; cva; stroKe; stroke |
| DOID:2030 | 12084 | ANXIETY; Anxiety; Anxiety Disorder; Anxiety state; anxiety; anxiety disorder; anxiety state; anxiety syndrome; anxiety-state |
| DOID:1612 | 10583 | BREAST CANCER; BReast CAncer; BReast Cancer; Breast Cancer; Breast cancer; Breast tumor; Breast-cancer; Primary breast cancer; breast Cancer; breast caNcEr; breast cancer; breast tumor; breast-cancer; breastcancer; mammary cancer; mammary tumor; primary breast cancer |
| DOID:2841 | 10021 | ASTHMA; Asthma; BHR; Bronchial hyper-reactivity; Bronchial hyperreactivity; EIA; Exercise-induced asthma; asthma; bronchial hyper reactivity; bronchial hyper-reactivity; bronchial hyperreactivity; exercise induced asthma; exercise-induced asthma |
| DOID:3083 | 9782 | CHRONIC OBSTRUCTIVE PULMONARY DISEASE; COLD; COPD; COPd; Chronic Obstructive Lung Disease; Chronic Obstructive Lung disease; Chronic Obstructive Pulmonary Disease; Chronic Obstructive Pulmonary disease; Chronic Obstructive lung Disease; Chronic Obstructive pulmonary Disease; Chronic Obstructive pulmonary disease; Chronic obstructive airway disease; Chronic obstructive lung disease; Chronic obstructive pulmonary disease; Cold; chronic Obstructive Lung Disease; chronic obstructive airway disease; chronic obstructive lung disease; chronic obstructive pulmonary disease; chronic obstructive pulmonary disorder; cold; copd |
| DOID:9970 | 9303 | OBESITY; OBesity; Obesity; obEsity; obe-sity; obesity |
| DOID:10763 | 9144 | HBP; HTN; HYPERTENSION; High Blood Pressure; High blood pressure; High-blood pressure; Hypertension; Hypertensive disease; high blood Pressure; high blood pressure; high blood-pressure; htn; hyper-tension; hypertension; hypertensive disease; hypertensive disorder |
| DOID:3393 | 6816 | C-HD; CAD; CHD; CORONARY ARTERY DISEASE; CORONARY SYNDROME; CORONARY syndrome; ChD; Coronary ARtery DIsease; Coronary Artery Disease; Coronary Disease; Coronary Heart Disease; Coronary Heart disease; Coronary Syndrome; Coronary artery disease; Coronary disease; Coronary heart disease; Coronary-artery-disease; coronary Syndrome; coronary arteriosclerosis; coronary artery dis-ease; coronary artery disease; coronary disease; coronary heart disease; coronary syndrome; coronary-artery disease; coronary-artery-disease |
| DOID:0060145 | 6115 | ANALGESIA; Analgesia; analgeSia; analgesia |
| DOID:0111084 | 5958 | FACE; FaCE; Face; face |
| DOID:9352 | 5848 | Diabetes Mellitus Type 2; Diabetes Mellitus Type II; Diabetes Mellitus type 2; Diabetes Mellitus, Type II; Diabetes mellitus Type 2; Diabetes mellitus non-insulin-dependent; Diabetes mellitus type 2; Diabetes mellitus type II; NIDDM; Non-Insulin Dependent Diabetes Mellitus; Non-Insulin-Dependent-Diabetes Mellitus; Non-insulin dependent diabetes mellitus; Non-insulin-dependent Diabetes Mellitus; Type 2 - Diabetes Mellitus; Type 2 Diabetes; Type 2 Diabetes Mellitus; Type 2 Diabetes mellitus; Type 2 diabetes; Type 2 diabetes mellitus; Type 2-diabetes mellitus; Type II Diabetes; Type II Diabetes Mellitus; Type II Diabetes mellitus; Type II diabetes; Type II diabetes mellitus; Type-2 Diabetes; Type-2 Diabetes Mellitus; Type-2 diabetes; Type-2 diabetes mellitus; Type-2-diabetes; Type-II diabetes; Type2 Diabetes Mellitus; Type2 diabetes; Type2 diabetes mellitus; diabetes mellitus type 2; diabetes mellitus type II; diabetes mellitus type-2; diabetes mellitus type2; diabetes mellitus, type 2; maturity onset diabetes; maturity-onset diabetes; non insulin dependent diabetes mellitus; non insulin-dependent diabetes mellitus; non-insulin dependent diabetes mellitus; non-insulin-dependent diabetes mellitus; noninsulin-dependent diabetes mellitus; type -2 diabetes mellitus; type 2 Diabetes; type 2 Diabetes Mellitus; type 2 diabetes; type 2 diabetes mellitus; type 2-diabetes; type 2diabetes; type 2diabetes mellitus; type II Diabetes; type II Diabetes Mellitus; type II diabetes; type II diabetes mellitus; type II-diabetes; type-2 Diabetes; type-2 diabetes; type-2 diabetes mellitus; type-2-diabetes; type-II diabetes; type-II diabetes mellitus; type-II- diabetes mellitus; type2 diabetes; type2 diabetes mellitus |
| DOID:10283 | 5056 | Familial Prostate Cancer; HPC; PRostate Cancer; Prostate CAncer; Prostate Cancer; Prostate cancer; Prostatic cancer; hereditary prostate cancer; prostate Cancer; prostate cancer; prostate-cancer; prostatic cancer |
| DOID:8469 | 4985 | FLU; Flu; Influenza; flu; influenza |
| DOID:225 | 4962 | SYNDROME; Syndrome; syn drome; syndrome |
| DOID:3908 | 4959 | NSCLC; Non Small Cell Lung Cancer; Non Small Cell Lung Carcinoma; Non Small Cell Lung cancer; Non small cell lung cancer; Non small-cell lung cancer; Non- small cell lung cancer; Non-Small Cell Lung Cancer; Non-Small Cell Lung Carcinoma; Non-Small Cell Lung cancer; Non-Small cell lung cancer; Non-Small- Cell Lung Cancer; Non-Small-Cell Lung Cancer; Non-Small-Cell lung Cancer; Non-small Cell Lung Cancer; Non-small Cell Lung Carcinoma; Non-small cell Lung Cancer; Non-small cell lung cancer; Non-small cell lung carcinoma; Non-small-cell Lung Cancer; Non-small-cell lung cancer; nSCLC; non small cell lung cancer; non small cell lung carcinoma; non small-cell lung cancer; non- small cell lung cancer; non-small Cell Lung Cancer; non-small cell Lung cancer; non-small cell lung Cancer; non-small cell lung cancer; non-small cell lung carcinoma; non-small-cell lung cancer; non-small-cell lung carcinoma; non-small-cell lung-cancer; nonsmall cell lung cancer; nonsmall cell lung cancer; nonsmall- cell lung cancer |
| DOID:784 | 4841 | CKD; CKF; CRD; CRF; Chronic Kidney Disease; Chronic Kidney disease; Chronic Kidney failure; Chronic Renal Disease; Chronic kidney disease; Chronic kidney failure; Chronic renal disease; chronic Kidney disease; chronic kidney disease; chronic kidney failure; chronic renal disease; chronic renal failure syndrome; ckd; crf; renal failure chronic |
Sort synonyms terms by frequency.
| nct_id | doid | N_mentions | disease_terms |
|---|---|---|---|
| NCT00000102 | DOID:0111161 | 1 | can |
| NCT00000102 | DOID:0050811 | 1 | congenital adrenal hyperplasia |
| NCT00000105 | DOID:11338 | 6 | tetanus;Tetanus |
| NCT00000113 | DOID:11830 | 14 | myopia;Myopia;nearsightedness |
| NCT00000113 | DOID:9835 | 1 | refractive error |
| NCT00000113 | DOID:1432 | 1 | blindness |
| NCT00000114 | DOID:10584 | 1 | Retinitis pigmentosa |
| NCT00000114 | DOID:8499 | 1 | night blindness |
| NCT00000114 | DOID:8466 | 1 | retinal degeneration |
| NCT00000114 | DOID:4 | 1 | disease |
| NCT00000115 | DOID:4447 | 5 | cystoid macular edema |
| NCT00000115 | DOID:13141 | 5 | uveitis;Uveitis |
| NCT00000115 | DOID:1686 | 2 | glaucoma |
| NCT00000115 | DOID:4 | 2 | disease |
| NCT00000115 | DOID:0111161 | 1 | can |
| NCT00000115 | DOID:8947 | 1 | Diabetic Retinopathy |
| NCT00000115 | DOID:1432 | 1 | visual impairment |
| NCT00000115 | DOID:83 | 1 | cataract |
| NCT00000116 | DOID:4 | 2 | disease |
| NCT00000116 | DOID:0111161 | 1 | can |
Keep only studies including both disease and drug mentions.